Soil pH determines the shift of key microbial energy metabolic pathways associated with soil nutrient cycle

Soil pH is one of the most important factors influencing microbial activity and function. In agricultural land, soil acidification results in decline of microbial abundance and diversity, and is associated with increased N₂O emissions. Moreover, soil pH is a crucial factor determining the effect of fertilizer on soil microbial abundance and functionality. However, the interaction effect of soil pH and the application of fertilizer on the abundance of key metabolic pathways involved in nitrogen, carbon, and sulfur cycles remains unclear. Therefore, we modified the original pH of soil (pH 6.0) to pH 4.5 by adding elemental sulfur to the soil and compared the effects of chemical (urea), organic fertilizer (concentrated vinasse), and the combination of both (urea and concentrated vinasse) on soil microbial functions under low soil pH (pH 4.5) and high soil pH (pH 6.0) conditions. Shotgun metagenome sequencing was conducted to obtain microbial functional gene abundance, and the data were analyzed using a model-based statistical approach to determine potential interactions among energy metabolic pathways (i.e., nitrogen, sulfur, methane metabolisms, and carbon fixation). Our result showed the strong effect of soil pH rather than the interaction effect of soil pH and fertilizer treatments on functional gene composition involved in microbial energy metabolisms. Furthermore, we determined nitrogen metabolism most affected by soil pH followed by the sulfur metabolism, methane metabolism, and carbon fixation. When relative abundances of microbial genes were averaged among fertilizer treatments, high soil pH increased gene abundance potentially associated with amino acid synthesis, while low pH increased gene abundance related to denitrifiers denitrification. N₂O emissions were higher under high soil pH conditions, suggesting a small contribution of denitrifiers to N₂O emissions. Among the fertilizer treatments, urea differently impacted gene abundance associated with N₂O and CH₄ emission depending on soil pH. This study provides an overview of microbial metabolic pathways influenced by soil pH and fertilizer treatments, specifically focusing on the microbial functions associated with soil environmental processes.